// $Id$
//
//  Copyright (C) 2005-2006 Rational Discovery LLC
//
//   @@ All Rights Reserved @@
//  This file is part of the RDKit.
//  The contents are covered by the terms of the BSD license
//  which is included in the file license.txt, found at the root
//  of the RDKit source tree.
//
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include "FeatTreeUtils.h"
#include "FeatTree.h"
#include <vector>
#include <algorithm>
#include <boost/graph/graph_utility.hpp>

namespace RDKit {
namespace FeatTrees {
typedef boost::property_map<FeatTreeGraph, FeatTreeEdge_t>::type
    FeatTreeEdgePMap;

FeatTreeGraphSPtr molToBaseTree(const ROMol &mol) {
  FeatTreeGraphSPtr resGraph(new FeatTreeGraph());

  // EFF: This can almost certainly be done with a single pass through
  // the atoms and rings, for now we're just trying to get it right

  // ------ ------ ------ ------
  // add a node to the initial feature tree for each of the SSSR rings:
  // ------ ------ ------ ------
  addRingsAndConnectors(mol, *resGraph);

  // ------ ------ ------ ------
  // Reduce any fused ring systems that form cycles in
  // the FeatTree to single points:
  // ------ ------ ------ ------
  replaceCycles(*resGraph);

  // ------ ------ ------ ------
  // We have not yet added bonds between ring systems, like
  // the N-N bond in:
  //    C1CN1-N1CC1
  // So loop over the rings that we currently have and add
  // those bonds as appropriate:
  // ------ ------ ------ ------
  addRingRingBonds(mol, *resGraph);

  // ------ ------ ------ ------
  // Now go through the molecule and add every non-ring atom that
  // has more than one neighbor; we include Hs in the neighbor count
  // ------ ------ ------ ------
  std::vector<unsigned int> atomIndices;
  atomIndices = addNonringAtoms(mol, *resGraph);

  // ------ ------ ------ ------
  // At this point all atom and ring nodes have been added to
  // the graph.
  // Add the atom-atom and atom-ring edges:
  // ------ ------ ------ ------
  addBondsFromNonringAtoms(mol, *resGraph, atomIndices);

  // ------ ------ ------ ------
  // Go through the graph and add zero nodes
  //  (points not associated with atoms that are used to
  //  break cycles caused by non-ring atoms bonding to rings)
  // ------ ------ ------ ------
  addZeroNodes(*resGraph);

  return resGraph;
}

void baseTreeToFeatTree(FeatTreeGraph &baseTree) {}

}  // end of namespace FeatTrees
}  // namespace RDKit